Mayor Jean Quan, left, and new city administrator Fred Blackwell listen to public comment on the DAC. Opponents of the Domain Awareness Center proposed for Oakland, Calif., came to voice their displeasure with the plan at the city council meeting on Tuesday, March 4, 2014. less

Mayor Jean Quan, left, and new city administrator Fred Blackwell listen to public comment on the DAC. Opponents of the Domain Awareness Center proposed for Oakland, Calif., came to voice their displeasure with ... more

City Economic Director, Fred Blackwell and Mayor Jean Quan, as the Oakland City Council went on to approve the budget proposal to make a drastic $28 million cut to its current budget, eliminating about 100 jobs in a major city reorganization prompted by the loss of redevelopment funds. in Oakland, Ca. on Tuesday January 31, 2012. less

City Economic Director, Fred Blackwell and Mayor Jean Quan, as the Oakland City Council went on to approve the budget proposal to make a drastic $28 million cut to its current budget, eliminating about 100 jobs ... more

Photo: Michael Macor, SFC

Image 4 of 5

Oakland City Administrator, Deanne Santana, (left) Mayor Jean Quan and Assistant city manager, Fred Blackwell give details of their budget proposal for the City of Oakland, during a press conference at City Hall in downtown Oakland, Ca. on Wednesday April 18, 2013. less

Oakland City Administrator, Deanne Santana, (left) Mayor Jean Quan and Assistant city manager, Fred Blackwell give details of their budget proposal for the City of Oakland, during a press conference at City ... more

New Oakland City Manager Fred Blackwell, listens to public comment about the DAC on Tuesday. Opponents of the Domain Awareness Center proposed for Oakland, Calif., came to voice their displeasure with the plan at the city council meeting on Tuesday, March 4, 2014. less

New Oakland City Manager Fred Blackwell, listens to public comment about the DAC on Tuesday. Opponents of the Domain Awareness Center proposed for Oakland, Calif., came to voice their displeasure with the plan ... more

Fred Blackwell, the Oakland official who only a month ago became the city's top administrator, has accepted a job as the CEO of a major Bay Area philanthropic organization, a move that hurts the struggling administration of Mayor Jean Quan.

Blackwell, 44, will take the reins of the San Francisco Foundation, a 66-year-old group that grants tens of millions of dollars a year to community organizations across the region. He starts that job in June, a departure that analysts said could prove detrimental to Quan's re-election, particularly after the stormy resignation of the previous city administrator, Deanna Santana.

"Given the ... (November) election, the timing couldn't be worse for her. This could be part of a referendum on her leadership," said David McCuan, a professor of political science at Sonoma State University. "It looks like the ship is leaking."

Blackwell's move also sounds a cautionary note for those who hope to succeed Quan, "as it shows what a difficult job it is to run that city," McCuan said.

The news also comes as Quan's administration searches for a permanent police chief to replace Howard Jordan, who left in May.

'Happy for Fred'

In a statement Wednesday after learning of Blackwell's departure, Quan said she was "happy for Fred and this great opportunity for him. I hope Oakland will join me in congratulating him on this achievement."

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She said she will appoint retired City Administrator Henry Gardner as an interim administrator when Blackwell leaves in June. Gardner was Oakland's administrator from 1981 to 1993.

Blackwell, who joined Oakland in October 2011 as the assistant city administrator, has been a key official in luring developers to the city and in trying to keep its professional sports teams in town.

He has been a key negotiator in the city's effort to hold onto the A's and build a new ballpark for the team near the city's waterfront, as well as constructing a stadium for the Raiders as part of a proposed Coliseum City project.

Blackwell's exit raises questions about how Oakland will continue to negotiate with the teams as they pursue more lucrative deals. The Raiders and A's declined to comment Wednesday on the city administrator's departure.

In a recent interview, Blackwell said the city administrator's position in his native city was the job he had wanted since he was a teen.

"It is no secret that we are a bare-knuckle town when it comes to politics," Blackwell said in March. "Tough decisions have to get made; criticism comes your way. If I am going to be under that level of scrutiny, if I am going to be that intense, if I am going to be spending time away from my family, I've got to be doing it for a place that I love."

Decision to leave

On Wednesday, he explained his decision to leave to Quan.

"I have been put into a tough position where I have been offered two dream jobs," Blackwell told The Chronicle, adding that he would be on call to help Oakland with its sports team issues even after he leaves for the foundation.

Doug Boxer, who has worked on a proposal to build a ballpark for the A's at the city's Howard Terminal, said Blackwell's departure wouldn't affect the project.

Still, Oakland political consultant Larry Tramutola said Blackwell's departure sends another signal to residents that Oakland's government is unstable and chaotic.

Oakland Councilman Noel Gallo said he was "completely surprised" that Blackwell was leaving.

"It is a great loss for the city of Oakland considering the challenges," Gallo said.

Andy Ballard, the chairman of the San Francisco Foundation's board of trustees, said he expected Blackwell would leave Oakland on good terms because part of the foundation's mission is to help that community. In 2012, the foundation distributed $89 million in grants across five Bay Area counties.

Across the bay

In San Francisco, Mayor Ed Lee steered clear of the political impact to his friend and fellow mayor across the bay, focusing instead on how Blackwell's appointment to the foundation "is not just good for the city, but he'll be a great asset to the entire region."

"Fred Blackwell is a very talented individual and I am pleased that he is coming back to San Francisco," Lee said in a statement. "I'm looking forward to working with him, especially on the critical issues that face San Francisco, like affordability, income inequality and housing."

Blackwell said he applied for the foundation job in November while he was still the assistant city administrator. But he didn't tell Quan, he said, because he didn't think he would be offered the job.

"I was pretty surprised when I got the offer," he said.

'Actively' pursued

Ballard said his organization "actively went after" Blackwell beginning in early January, when he was still the assistant city administrator. "He didn't come after us."

"Fred has been dedicated to the work he has been doing in Oakland," Ballard said. "My perspective is that he was the logical successor to take that (city administrator) job and had this job not been available, my hunch is that Fred would have been delighted to do that work, and he really cares deeply about that work."

Blackwell replaces Sandra Hernandez, who announced in August that she was leaving the foundation after 16 years at the helm to become president and CEO of the California HealthCare Foundation. During her term, the foundation granted $1.2 billion to Bay Area organizations.

In the fall, the foundation began a nationwide search for her successor.

"Unanimously, Fred really rose to the top of the group we spoke to," Ballard said. "He's got an unbelievably deep commitment to this community and all the communities we serve. He has that in a way that we found incredibly compelling."

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